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Results for “trajectory analysis”

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At least 217 records · Page 12Linked to original sources

PubMed2000

Structure and hydration of BamHI DNA recognition site: a molecular dynamics investigation.

The results of a 3-ns molecular dynamics simulation of the dodecamer duplex d(TATGGATCCATA)(2) recognized by the BamHI endonuclease are presented here. The DNA has been simulated as a flexible molecule using an AMBER force field and the Ewald summation method, which eliminates the undesired effects of truncation and permits evaluation of the full effects of electrostatic forces. The starting B conformation evolves toward a configuration quite close to that observed through x-ray diffraction in its complex with BamHI. This configuration is fairly stable and the Watson-Crick hydrogen bonds are well maintained over the simulation trajectory. Hydration analysis indicates a preferential hydration for the phosphate rather than for the ester oxygens. Hydration shells in both the major and minor groove were observed. In both grooves the C-G pairs were found to be more hydrated than A-T pairs. The "spine of hydration" in the minor groove was clear. Water residence times are longer in the minor groove than in the major groove, although relatively short in both cases. No special long values are observed for sites where water molecules were observed by x-ray diffraction, indicating that water molecules having a high probability of being located in a specific site are also fast-exchanging.

Base Pairing↗

PubMed1988

Application of Brownian motion theory to the analysis of membrane channel ionic trajectories calculated by molecular dynamics.

This paper shows how Brownian motion theory can be used to analyze features of individual ion trajectories in channels as calculated by molecular dynamics, and that its use permits more precise determinations of diffusion coefficients than would otherwise be possible. We also show how a consideration of trajectories of single particles can distinguish between effects due to the magnitude of the diffusion coefficient and effects due to barriers and wells in the potential profile, effects which can not be distinguished by consideration of average fluxes.

Chemical Phenomena↗

PubMed1999

Free Brownian motion of individual lipid molecules in biomembranes.

The mobility of phospholipids in free-standing and supported membranes was investigated on the level of individual molecules. For the analysis of trajectories a new statistical treatment was developed that permitted us to clearly distinguish different types of diffusional motion. A freely diffusing subfraction of lipids within supported membranes was identified. Its mobility was characterized by a mean lateral diffusion constant of D(supp) = 4.6 microm(2)/s. In comparison, the mobility of lipids embedded in "free-standing" planar membranes yielded an increase in the mean diffusion constant by a factor of 4.5, D(free) = 20.6 microm(2)/s. This increase is attributed to the ultrathin (<or=1 nm) lubricating water layer between membranes and glass support.

Cell Membrane↗

PubMed1999

Real-time imaging of the dynamics of secretory granules in growth cones.

Secretory granules containing a hybrid protein consisting of the regulated secretory protein tissue plasminogen activator and an enhanced form of green fluorescent protein were tracked at high spatial resolution in growth cones of differentiated PC12 cells. Tracking shows that granules, unlike synaptic vesicles, generally are mobile in growth cones. Quantitative analysis of trajectories generated by granules revealed two dominant modes of motion: diffusive and directed. Diffusive motion was observed primarily in central and peripheral parts of growth cones, where most granules diffused two to four orders of magnitude more slowly than comparably sized spheres in dilute solution. Directed motion was observed primarily in proximal parts of growth cones, where a subset of granules underwent rapid, directed motion at average speeds comparable to those observed for granules in neurites. This high-resolution view of the dynamics of secretory granules in growth cones provides insight into granule organization and release at nerve terminals. In particular, the mobility of granules suggests that granules, unlike synaptic vesicles, are not tethered stably to cytoskeletal structures in nerve terminals. Moreover, the slow diffusive nature of this mobility suggests that secretory responses involving centrally distributed granules in growth cones will occur slowly, on a time scale of minutes or longer.

Animals↗

PubMed2002

Atmospheric transport patterns and possible consequences for the European North after a nuclear accident.

The main purpose of this study is to examine possible impacts and consequences of a hypothetical accident at the Kola nuclear plant in north-west Russia on different geographical regions: Scandinavia, central Europe, European FSU and Taymyr. The period studied is 1991-1996. An isentropic trajectory model has been used to calculate forward trajectories that originated over the nuclear accident region. Atmospheric transport patterns were identified using the isentropic trajectories and a cluster analysis technique. From the trajectory model results, a number of cases were chosen for examination in detail using more complete transport models. For this purpose, the models MATHEW/ADPIC, DERMA and a newly developed FOA Random Displacement Model have been used to simulate the radionuclide transport and contamination in the case of a nuclear accident and their results have been compared with those of the trajectory modelling. Estimation of the long-term consequences for populations after an accident has been performed for several specific dates by empirical models and correlation between fallout and doses to humans on the basis of the Chernobyl accident exposures in Scandinavia.

Air Movements↗

PubMed2001

The social context of health selection: a longitudinal study of health and employment.

Health selection out of the labour force has received considerable attention by analysts attempting to disentangle the "true" biological dimensions of ill-health from its social meaning. Rejecting this dualistic separation, we argue that the effect of health on labour force participation is an inherently social process reflecting differential access to material and symbolic rewards that are structured by social position. Using longitudinal data from the US-based Panel Study of Income Dynamics, we examine the extent to which structural arrangements, including those designated by gender, race, education and age, differentially affect the risk of a labour market exit when health is compromised. Individuals employed at entry into the study (from 1984-1990) were followed for the duration of the study or until they left the labour force. Analyses were stratified by gender and age (25-39 and 40-61 years at baseline). We found suggestive evidence that the hazard of labour market exit in the context of perceived ill-health depended on gender, race and education, but in ways that were not constant across each of these social positions. For example, men may be more vulnerable to the labour market effects of poor health, but only in the younger group, black men were less likely to leave the labour force than white men, and education mattered, but only among younger women and older men. While these patterns may reflect differential access to disability pensions or other work-related benefits, we suggest that a more detailed analysis of trajectories of health and employment. as well as the meaning of health states would be useful in further elucidating the social dimensions of health selection.

Adult↗

PubMed2003

Resonant excitation in a low-pressure linear ion trap.

It has been shown that through the process of resonant excitation the fragmentation of ions confined in a low-pressure (<0.05 mTorr) linear ion trap (LIT) can be accomplished while maintaining both high fragmentation efficiency and high resolution of excitation. The ion reserpine, 609.23 Da, has been fragmented with efficiencies greater than 90% while a higher mass ion, a homogeneously substituted triazatriphosphorine of mass 2721.89 Da, has been fragmented with 48% efficiency. This was accomplished by extended resonant excitation by low-amplitude auxiliary RF signals. Computer modelling of ion trajectories and analysis of the trapping potentials have demonstrated that a reduction in neutralization of ions on the rods (or losses on the rods) and increased fragmentation is a consequence of higher order terms in the potential introduced by the round-rod geometry of the LIT.

Journal Article↗

PubMed2026

Early-stage trajectories of social-occupational functioning and long-term functional outcome prediction in early psychosis: A 12-year follow-up of the randomized controlled trial on extended early intervention.

BACKGROUND: Functional impairment in psychosis often persists despite symptomatic remission. There is a paucity of research examining early-course psychosocial functioning trajectories, and none has been conducted to examine relationship between the trajectories and prospective long-term functional outcomes in early psychosis sample. METHODS: We conducted 12-year follow-up of a randomized controlled trial on extended early intervention for first-episode psychosis to identify early-course social-occupational functioning trajectories and their baseline predictors and associations with 12-year outcomes. Participants who completed Social and Occupational Functioning Scale (SOFAS) scores at three or more timepoints between baseline and 3-year follow-up were included in the study. Premorbid adjustment, illness characteristics, symptom severity, functioning, and treatment profiles were assessed. Latent growth mixture modeling was employed to derive early-course social-occupational functioning trajectories based on SOFAS scores over 3-year follow-up. RESULTS: A total of 148 participants were included in this study, with 106 patients having completed the 12-year follow-up. Our results identified four distinct trajectories, including persistently-good class, gradually-improved class, suboptimal-stable class, and persistently-poor class. Patients in persistently-poor class had more severe negative symptoms at baseline compared to patients in persistently-good class. Patients with persistently-poor trajectory had worse long-term outcomes than those with other classes in the majority of functional measures at 12-year follow-up. CONCLUSIONS: The majority of patients were classified in early-stage suboptimal or poor functional trajectories. Above one-fourth of the participants exhibited persistently-poor social-occupational functioning trajectory, which predicted worse functional outcomes at 12-year follow-up. These findings highlighted the importance of tracking functional changes during the initial years of illness.

Humans↗

PubMed2005

Structure and dynamics of the hydrogen-bond network around (R,R)-pterocarpans with biological activity in aqueous solution.

Molecular dynamics simulations were carried out in the presence of 2380 water molecules (TIP3P) to explore the conformational preferences of 3,9-dimethoxy-4-prenylpterocarpan (bitucarpin A) and 3,9-dihydroxy-4,8-diprenylpterocarpan (erybraedin C) and the H-bond network around them, using the empirical general AMBER force field (GAFF). Specific angle and torsional parameters have been improved in order to match the geometries of the minimum energy structures obtained from an earlier DFT/ab initio study in vacuo, taking into account a few configurations [Alagona, G.; Ghio, C.; Monti, S. Phys. Chem. Chem. Phys. 2004, 6, 2849-2857]. RESP partial charges were assigned to reproduce the electrostatic potential determined at the HF/6-31G level of theory. The analysis of trajectories allowed the conformations of bitucarpin and erybraedin as well as the distribution of water molecules around them to be elucidated. During one of the simulations only, the scaffold of erybraedin undergoes interconversion from its most stable Ht conformation to the Ot one and vice versa. Radial distribution functions, coordination numbers, and angular distributions put forward the extent of solvent structure and the hydrogen bonding behavior of their various (methoxy, hydroxyl, or ethereal) oxygen atoms. The distribution of solvent molecules in the first and second solvation shells as well as the residence times for the different solute-solvent interacting sites have been considered.

Hydrogen Bonding↗

PubMed2006

Data mining of molecular dynamics trajectories of nucleic acids.

Analysis, storage, and transfer of molecular dynamic trajectories are becoming the bottleneck of computer simulations. In this paper we discuss different approaches for data mining and data processing of huge trajectory files generated from molecular dynamic simulations of nucleic acids.

Computer Simulation↗

PubMed2001

The investigation of the effects of counterions in protein dynamics simulations.

Molecular simulations able to exactly represent solvated charged proteins are helpful in understanding protein dynamics, structure and function. In the present study we have used two different starting structures of papain (a typical, stable, globular protein of intermediate net charge) and different modeling procedures to evaluate some effects of counterions in simulations. A number of configurations have been generated and relaxed for each system by various combinations of constrained simulated annealing and molecular dynamics procedures, using the AMBER force field. The analysis of trajectories shows that the simulations of solvated proteins are moderately sensitive to the presence of counterions. However, this sensitivity is highly dependent on the starting model and different procedures of equilibration used. The neutralized systems tend to evince smaller root mean square deviations regardless of the system investigated and the simulation procedure used. The results of parameterized fitting of the simulated structures to the crystallographic data, giving quantitative measure of the total charge influence on the stability of various elements of the secondary structure, revealed a clear scatter of different reactions of various systems' secondary structures to counterions addition: some systems apparently were stabilized when neutralized, while the others were not. Thus, one cannot unequivocally state, despite consideration of specific simulation conditions, whether protein secondary structures are more stable when they have neutralized charges. This suggests that caution should be taken when claiming the stabilizing effect of counterions in simulations other than those involving small, unstable polypeptides or highly charged proteins.

Computer Simulation↗

PubMed2005

Classical effects of laser pulse duration on strong-field double ionization.

We use classical electron ensembles and the aligned-electron approximation to examine the effect of laser pulse duration on the dynamics of strong-field double ionization. We cover the range of intensities 10(14)-10(16) W/cm2 for the laser wavelength 780 nm. The classical scenario suggests that the highest rate of recollision occurs early in the pulse and promotes double-ionization production in few-cycle pulses. In addition, the purely classical ensemble calculation predicts an exponentially decreasing recollision rate with each subsequent half cycle. We confirm the exponential behavior by trajectory back analysis.

Journal Article↗

PubMed1999

Mauthner and reticulospinal responses to the onset of acoustic pressure and acceleration stimuli.

We determined how the Mauthner cell and other large, fast-conducting reticulospinal neurons of the goldfish responded to acoustic stimuli likely to be important in coordinating body movements underlying escape. The goal was to learn about the neurophysiological responses to these stimuli and the underlying processes of sensorimotor integration. We compared the intracellularly recorded postsynaptic responses (PSPs) of 9 Mauthner cells and a population of 12 other reticulospinal neurons to acoustic pressure and acceleration stimuli. All recorded cells received both pressure and acceleration inputs and responded to stimuli regardless of initial polarity. Thus these cells receive acoustic components necessary to determine source direction. We observed that the Mauthner cell was broadly tuned to acoustic pressure from 100 to 2,000 Hz, with a Q(10dB) of 0.5-1.1 over the best frequency range, 400-800 Hz. This broad tuning is probably due to input from S1 afferents and is similar to tuning of the behavioral audiogram. Our data suggest that cells have relatively more sustained responses to acceleration than to pressure stimuli, to which they rapidly adapted. For a given cell, PSP latencies and amplitudes varied inversely with stimulus intensity. For the entire population of cells studied, minimum onset latencies (i.e., those at the highest intensities) ranged from 0.7 to 7.6 ms for acoustic pressure and 0.7 to 9.8 ms for acceleration. This distribution in minimum onset latencies is consistent with earlier EMG and kinematic findings and supports our previous hypothesis that escape trajectory angle is controlled, in part, by varying the activation time of neurons in the escape network. While the Mauthner cell latency did not differ to both onset polarities of pressure and acceleration, this was not true of all cells. Also, the Mauthner cell responses to pressure were approximately 0.6 ms faster than to acceleration; for the other cells, this difference was 1.1 ms with some cells having differences </=3 ms. To both pressure and acceleration, the average, minimum Mauthner cell latency was approximately 1 ms faster than the average of the 12 other cells. These data are consistent with the hypothesis that the Mauthner cell fires first, followed by other reticulospinal neurons, which more finely regulate escape trajectory. Finally, analysis of our results suggests that while pressure is more important in depolarizing the cell near threshold, high levels of acceleration, perhaps from fluid flow, may be very important in activating the system in a directional manner.

Acceleration↗

PubMed2006

Minor groove deformability of DNA: a molecular dynamics free energy simulation study.

The conformational deformability of nucleic acids can influence their function and recognition by proteins. A class of DNA binding proteins including the TATA box binding protein binds to the DNA minor groove, resulting in an opening of the minor groove and DNA bending toward the major groove. Explicit solvent molecular dynamics simulations in combination with the umbrella sampling approach have been performed to investigate the molecular mechanism of DNA minor groove deformations and the indirect energetic contribution to protein binding. As a reaction coordinate, the distance between backbone segments on opposite strands was used. The resulting deformed structures showed close agreement with experimental DNA structures in complex with minor groove-binding proteins. The calculated free energy of minor groove deformation was approximately 4-6 kcal mol(-1) in the case of a central TATATA sequence. A smaller equilibrium minor groove width and more restricted minor groove mobility was found for the central AAATTT and also a significantly ( approximately 2 times) larger free energy change for opening the minor groove. The helical parameter analysis of trajectories indicates that an easier partial unstacking of a central TA versus AT basepair step is a likely reason for the larger groove flexibility of the central TATATA case.

Algorithms↗

PubMed2006

Developmental trajectories of adolescent popularity: a growth curve modelling analysis.

Growth curve modelling was used to examine developmental trajectories of sociometric and perceived popularity across eight years in adolescence, and the effects of gender, overt aggression, and relational aggression on these trajectories. Participants were 303 initially popular students (167 girls, 136 boys) for whom sociometric data were available in Grades 5-12. The popularity and aggression constructs were stable but non-overlapping developmental dimensions. Growth curve models were run with SAS MIXED in the framework of the multilevel model for change [Singer, J. D., & Willett, J. B. (2003). Applied longitudinal data analysis. Oxford, UK: Oxford University Press]. Sociometric popularity showed a linear change trajectory; perceived popularity showed nonlinear change. Overt aggression predicted low sociometric popularity but an increase in perceived popularity in the second half of the study. Relational aggression predicted a decrease in sociometric popularity, especially for girls, and continued high-perceived popularity for both genders. The effect of relational aggression on perceived popularity was the strongest around the transition from middle to high school. The importance of growth curve models for understanding adolescent social development was discussed, as well as specific issues and challenges of growth curve analyses with sociometric data.

Adolescent↗

PubMed2006

Behavioral trajectories as predictors in event history analysis: male calling behavior forecasts medfly longevity.

A recent study on wild male Mediterranean fruit flies [Papadopoulos, N.T., Katsoyannos, B.I., Kouloussis, N.A., Carey, J.R., Müller, H.-G., Zhang, Y., 2004. High sexual signalling rates of young individuals predict extended life span in male Mediterranean fruit flies. Oecologia 138, 127-134] provided evidence that intense sexual signalling (calling behavior) is associated with longer life span. We demonstrate here an approach based on functional data analysis methodology for predicting individual remaining longevity and the distribution of remaining lifetime from individual behavioral trajectories. A key methodological concept is the time evolution of mean functions and eigenfunctions. This methodology is applied to the event history of calling behavior of male medflies. The results demonstrate complex relationships between male calling behavior and subsequent longevity that complement previous biodemographic analyses of these data. A high level of recent calling activity is found to be associated with increased remaining lifetime for an individual male fly, while calling activity at early ages plays no role for remaining longevity.

Animals↗

PubMed2005

Study of the insulin dimerization: binding free energy calculations and per-residue free energy decomposition.

A calculation of the binding free energy for the dimerization of insulin has been performed using the molecular mechanics-generalized Born surface area approach. The calculated absolute binding free energy is -11.9 kcal/mol, in approximate agreement with the experimental value of -7.2 kcal/mol. The results show that the dimerization is mainly due to nonpolar interactions. The role of the hydrogen bonds between the 2 monomers appears to give the direction of the interactions. A per-atom decomposition of the binding free energy has been performed to identify the residues contributing most to the self association free energy. Residues B24-B26 are found to make the largest favorable contributions to the dimerization. Other residues situated at the interface between the 2 monomers were found to make favorable but smaller contributions to the dimerization: Tyr B16, Val B12, and Pro B28, and to an even lesser extent, Gly B23. The energy decomposition on a per-residue basis is in agreement with experimental alanine scanning data. The results obtained from a single trajectory (i.e., the dimer trajectory is also used for the monomer analysis) and 2 trajectories (i.e., separate trajectories are used for the monomer and dimer) are similar.

Crystallography, X-Ray↗

PubMed2025

Inferring cell trajectories of spatial transcriptomics via optimal transport analysis.

The integration of cell transcriptomics and spatial position to organize differentiation trajectories remains a challenge. Here, we introduce SpaTrack, which leverages optimal transport to reconcile both gene expression and spatial position from spatial transcriptomics into the transition costs, thereby reconstructing cell differentiation. SpaTrack can construct detailed spatial trajectories that reflect the differentiation topology and trace cell dynamics across multiple samples over temporal intervals. To capture the dynamic drivers of differentiation, SpaTrack models cell fate as a function of expression profiles influenced by transcription factors over time. By applying SpaTrack, we successfully disentangle spatiotemporal trajectories of axolotl telencephalon regeneration and mouse midbrain development. Diverse malignant lineages expanding within a primary tumor are uncovered. One lineage, characterized by upregulated epithelial mesenchymal transition, implants at the metastatic site and subsequently colonizes to form a secondary tumor. Overall, SpaTrack efficiently advances trajectory inference from spatial transcriptomics, providing valuable insights into differentiation processes.

Animals↗